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The study applies high-performance parallel computing to compare whole genomes of Xanthomonas axonopodis pv. citri and Xanthomonas campestris pv. campestris, each exceeding five million base pairs. It builds a feasible parallel strategy on a 64-node Beowulf cluster, comparing homologous genes and regions/gaps, yielding less processing time and improved result quality over Blast and EGG-based approaches.",{"@graph":69,"@context":122},[70,84,105],{"@type":71,"itemListElement":72},"BreadcrumbList",[73,77,79,82],{"item":74,"name":75,"@type":76,"position":8},"https://docshare.wps.com","Home","ListItem",{"item":78,"name":9,"@type":76,"position":14},"https://docshare.wps.com/document/",{"item":80,"name":40,"@type":76,"position":81},"https://docshare.wps.com/document/research-report/",3,{"item":83,"name":65,"@type":76,"position":19},"https://docshare.wps.com/document/comparison-of-genomes-using-high-performance-parallel-computing/314286/",{"url":83,"name":65,"@type":85,"image":86,"author":91,"headline":65,"publisher":94,"fileFormat":97,"inLanguage":63,"description":67,"dateModified":98,"datePublished":99,"encodingFormat":97,"isAccessibleForFree":100,"interactionStatistic":101},"DigitalDocument",{"url":87,"@type":88,"width":89,"height":90},"https://docshare.wps.com/thumbnails/comparison-of-genomes-using-high-performance-parallel-computing/314286.png","ImageObject",300,407,{"name":92,"@type":93},"Well Done","Person",{"url":74,"name":95,"@type":96},"DocShare","Organization","application/pdf","2026-10-18","2026-09-20",true,{"@type":102,"interactionType":103,"userInteractionCount":34},"InteractionCounter",{"@type":104},"ViewAction",{"@type":106,"mainEntity":107},"FAQPage",[108,114,118],{"name":109,"@type":110,"acceptedAnswer":111},"What is the goal of comparing the two genomes in the paper?","Question",{"text":112,"@type":113},"The paper aims to identify common functionalities and better understand how genes or gene groups are organized and involved in multiple functions.","Answer",{"name":115,"@type":110,"acceptedAnswer":116},"Which genomes are compared using the parallel computing approach?",{"text":117,"@type":113},"It compares the whole genomes of Xanthomonas axonopodis pv. citri and Xanthomonas campestris pv. campestris.",{"name":119,"@type":110,"acceptedAnswer":120},"What does the parallel comparison strategy evaluate beyond homologous genes?",{"text":121,"@type":113},"In addition to homologous genes, it compares the regions or gaps between corresponding homologous genes using DNA nucleotide information.","https://schema.org",{"og:url":83,"og:type":124,"og:title":65,"og:site_name":95,"og:description":67},"article",{"robots":126,"canonical":83},"index,follow",{"doc_id":128,"site_id":62},314286,1789900505,{"code":4,"msg":5,"data":131},{"doc_id":128,"user_id":132,"nickname":92,"user_avatar":133,"doc_module":4,"category_id":39,"category_name":40,"doc_title":65,"doc_description":67,"doc_content":134,"file_id":135,"file_url":136,"file_type":137,"file_size":138,"view_count":34,"is_deleted":4,"is_public":8,"is_downloadable":8,"audit_status":8,"page_count":34,"language":139,"language_code":63,"site_id":62,"html_lang":63,"table_of_contents":140,"faqs":141,"seo_title":142,"seo_description":67,"update_tm":129,"read_time":143,"preview_page_count":4},5909892210082,"https://ap-avatar.wpscdn.com/avatar/56001069da27c9f41e8?x-image-process=image/resize,m_fixed,w_180,h_180&k=1789614185077863061","Comparison of Genomes using High-Performance Parallel Computing  \nN. F. Almeida Jr􀀃  \nUniv. Federal de Mato Grosso do Sul [nalvo@dct.ufms.br](nalvo@dct.ufms.br)  \nE. N. Caceres†  \nUniv. Federal de Mato Grosso do Sul [edson@dct.ufms.br](edson@dct.ufms.br)  \nC. E. R. Alves Universidade S˜ao Judas Tadeu  \nprof.carlos r [alves@usjt.br](alves@usjt.br)  \nS. W. Song‡  \nUniversidade de S˜ao Paulo [song@ime.usp.br](song@ime.usp.br)  \nAbstract  \nComparison of the DNA sequences and genes of two genomes can be useful to investigate the common functionalities of the corresponding organisms and get a better understanding of how the genes or groups of genes are organized and involved in several functions. In this paper we use high-performance parallel computing to compare the whole genomes of two organisms, namely Xanthomonas axonopodis pv. citri and Xanthomonas campestris pv. campestris, each with more than five million basepairs. Our purpose is two-fold. First we intend to exploit the high-performance power of a cluster of low-cost microcomputers, propose a parallel solution to this problem, and show its feasibility with implementation and performance results. Second we do additional comparisons of the two genomes by locating and compare not only the homologous genes (expressed in terms of the 20-letter amino acids) but also compare the regions or gaps (in terms of the 4-letter DNA nucleotides) between the corresponding homologous genes. We have implemented the proposed comparison strategy to compare the two genomes Xanthomonasaxonopodis pv. citri (Xac) and Xanthomonas campestris pv. campestris (Xcc). The parallel platform used is a Beowulf cluster of 64 nodes consisting of low cost microcomputers. Xac has 5,175,554 base pairs and 4,313 proteincoding genes while Xcc has 5,076,187 base pairs and 4,182 protein-coding genes. The parallel solution is based on the dynamic programming approach and presents not only less processing time, but also better quality results as compared to approaches based on Blast and EGG.  \n􀀃 Partially supported by CNPq.  \n† Partially supported by FINEP-PRONEX-SAI Proc. No. 76.97.1022.00, CNPq, FAPESP Proc. No. 1997/10982-0 .  \n‡ Partially supported by CNPq Grants No. 52.3778/96-1, 55.2028/02-9 .  \n1. Introduction  \nHigh-performance computing has always been associated with solutions ofthe so-called grand challenges that include such diverse areas as weather prediction, climate and global changes, material sciences, medicine and health, and more recently, the important area of bioinformatics. With recent advances of DNA sequencing technology, whole genomes of bacteria, archaea and eukaryota, including humans, have been sequenced, with the announcements of new sequencing results on a nearly monthly basis. The amount of genome information already available is astounding. According to the National Center for Biotechnology Information of the National Institute of Health, within 20 years after the creation of Genbank, the database has grown from 680 thousand base pairs in 1982 to 28.5 billion base pairs in 2002 [12] .  \nIn an area so overwhelmed by data and incomplete information we are urgently in need of high-performance computing tools to analyze and interpret the vast amount of raw data and fragments of information in order to get a better glimpse and understanding of at least some of the biological functions of living organisms.  \nThough an awesome and computationally expensive effort, comparison of the DNA sequences and genes of two whole genomes can be useful to investigate the common functionalities of the corresponding organisms and get abetter understanding of how the genes or groups of genes are organized and involved in several functions.  \nIn this paper we use high-performance parallel computing to compare the whole genomes of two organisms, namely Xanthomonas axonopodis pv. citri and Xanthomonas campestris pv. campestris, each with more than five million base-pairs.  \nA pioneer work along the line of compariso","cbCaiotQ6QqxvK4v","https://ap.wps.com/l/cbCaiotQ6QqxvK4v","pdf",111458,"English","# Abstract\n# 1. Introduction\n# 2. Basic Concepts","[{\"question\":\"What is the goal of comparing the two genomes in the paper?\",\"answer\":\"The paper aims to identify common functionalities and better understand how genes or gene groups are organized and involved in multiple functions.\"},{\"question\":\"Which genomes are compared using the parallel computing approach?\",\"answer\":\"It compares the whole genomes of Xanthomonas axonopodis pv. citri and Xanthomonas campestris pv. campestris.\"},{\"question\":\"What does the parallel comparison strategy evaluate beyond homologous genes?\",\"answer\":\"In addition to homologous genes, it compares the regions or gaps between corresponding homologous genes using DNA nucleotide information.\"}]","Comparison of Genomes using High-Performance Parallel Computing | PDF",18]